[1] "Preparing Project:"
[1] "Hereeeeee"
[1] "Creating Object from..."
[1] "Patient data:"
[1] FALSE
[1] "Reading expression:tcga_coad_cms1.rds"
class: RangedSummarizedExperiment 
dim: 63856 80 
metadata(8): time_created recount3_version ... annotation recount3_url
assays(1): raw_counts
rownames(63856): ENSG00000278704.1 ENSG00000277400.1 ...
  ENSG00000182484.15_PAR_Y ENSG00000227159.8_PAR_Y
rowData names(10): source type ... havana_gene tag
colnames(80): 196281bd-2c05-46d3-a53c-ead8639ef02d
  45cedf59-bc7a-4d86-8c2d-9a91ac141d30 ...
  bcd07f56-fa83-473f-b5d1-9c637299c7e2
  b444dc9f-6f2c-4cbc-9e1c-7b9e0fc790f2
colData names(937): rail_id external_id ... recount_seq_qc.errq
  BigWigURL
[1] "Map Barcodes..."
[1] "Normalize with CPM..."
[1] "LOG: There are 80 intial columns "
[1] "196281bd-2c05-46d3-a53c-ead8639ef02d"
[2] "45cedf59-bc7a-4d86-8c2d-9a91ac141d30"
[3] "771833ef-f9f3-43e9-ac9e-bf249333b257"
[4] "343f031b-0095-429d-8212-ad0581dbb05b"
[5] "aa49ac5d-9dc7-48f9-8498-deb9a3f0e0d0"
 [1] "TCGA-AA-3845-01A-01R-1022-07" "TCGA-F4-6570-01A-11R-1774-07"
 [3] "TCGA-G4-6588-01A-11R-1774-07" "TCGA-A6-3809-01A-01R-1022-07"
 [5] "TCGA-CM-5861-01A-01R-1653-07" "TCGA-AZ-4615-01A-01R-1410-07"
 [7] "TCGA-AA-3672-01A-01R-0905-07" "TCGA-A6-3809-01B-04R-A277-07"
 [9] "TCGA-AA-3516-11A-01R-A32Z-07" "TCGA-AA-A02R-01A-01R-A00A-07"
[11] "TCGA-AA-3815-01A-01R-1022-07" "TCGA-AA-3715-01A-01R-0905-07"
[13] "TCGA-D5-6540-01A-11R-1723-07" "TCGA-AZ-6601-01A-11R-1774-07"
[15] "TCGA-AA-3518-11A-01R-1672-07" "TCGA-AZ-4616-01A-21R-1839-07"
[17] "TCGA-AD-6895-01A-11R-1928-07" "TCGA-AA-3811-01A-01R-1022-07"
[19] "TCGA-AZ-6601-11A-01R-1774-07" "TCGA-AA-A00J-01A-02R-A002-07"
[21] "TCGA-CA-5254-01A-21R-1839-07" "TCGA-AA-3664-01A-01R-0905-07"
[23] "TCGA-AA-A00R-01A-01R-A002-07" "TCGA-A6-2672-01B-03R-2302-07"
[25] "TCGA-AA-3554-01A-01R-0826-07" "TCGA-A6-A565-01A-31R-A28H-07"
[27] "TCGA-D5-6930-01A-11R-1928-07" "TCGA-CK-4951-01A-01R-1410-07"
[29] "TCGA-CM-6674-01A-11R-1839-07" "TCGA-A6-3809-01A-01R-A278-07"
[31] "TCGA-AA-3994-01A-01R-1113-07" "TCGA-AA-A01P-01A-21R-A083-07"
[33] "TCGA-CM-6171-01A-11R-1653-07" "TCGA-AA-3710-01A-01R-1022-07"
[35] "TCGA-CK-6746-01A-11R-1839-07" "TCGA-AA-3877-01A-01R-1022-07"
[37] "TCGA-AA-A01R-01A-21R-A083-07" "TCGA-AA-A00E-01A-01R-A002-07"
[39] "TCGA-AU-6004-01A-11R-1723-07" "TCGA-AA-3821-01A-01R-1022-07"
[41] "TCGA-AA-3543-01A-01R-0826-07" "TCGA-AA-3492-01A-01R-1410-07"
[43] "TCGA-A6-6780-01A-11R-A278-07" "TCGA-CA-6718-01A-11R-1839-07"
[45] "TCGA-CM-6675-01A-11R-1839-07" "TCGA-AA-3525-11A-01R-A32Z-07"
[47] "TCGA-AA-A00A-01A-01R-A002-07" "TCGA-AA-3492-01A-01R-1410-07"
[49] "TCGA-AA-A01P-01A-21R-A083-07" "TCGA-AA-3555-01A-01R-0821-07"
[51] "TCGA-AA-3516-01A-02R-0826-07" "TCGA-A6-6780-01B-04R-A277-07"
[53] "TCGA-AA-3525-01A-02R-0826-07" "TCGA-DM-A1HB-01A-21R-A180-07"
[55] "TCGA-CK-5916-01A-11R-1653-07" "TCGA-AZ-6598-01A-11R-1774-07"
[57] "TCGA-D5-6928-01A-11R-1928-07" "TCGA-AA-A022-01A-21R-A16W-07"
[59] "TCGA-G4-6299-01A-11R-1774-07" "TCGA-A6-2672-01A-01R-0826-07"
[61] "TCGA-A6-2672-01B-03R-2302-07" "TCGA-AA-3930-01A-01R-1022-07"
[63] "TCGA-A6-6653-01A-11R-1774-07" "TCGA-AM-5821-01A-01R-1653-07"
[65] "TCGA-AZ-6598-11A-01R-1774-07" "TCGA-AD-5900-01A-11R-1653-07"
[67] "TCGA-A6-6780-01A-11R-1839-07" "TCGA-AA-3864-01A-01R-1022-07"
[69] "TCGA-AA-3966-01A-01R-1113-07" "TCGA-CM-4751-01A-02R-1839-07"
[71] "TCGA-CK-4951-01A-01R-1410-07" "TCGA-AZ-4615-01A-01R-1410-07"
[73] "TCGA-A6-2676-01A-01R-0826-07" "TCGA-CM-4743-01A-01R-1723-07"
[75] "TCGA-D5-6927-01A-21R-1928-07" "TCGA-CK-5913-01A-11R-1653-07"
[77] "TCGA-AA-3949-01A-01R-1022-07" "TCGA-G4-6628-01A-11R-1839-07"
[79] "TCGA-AA-3977-01A-01R-1022-07" "TCGA-AA-3518-01A-02R-0826-07"
[1] "LOG: There are  mapped columns  "
[1] "LOG: There are 70 non duplicate samples "
[1] "Batch correction for  tcga.gdc_platform"
[1] "LOG: There are 20266 genes that pass mintpm filtering "
[1] "Using logcpm..."
[1] "WARNING: no purity for "
[1] "LOG: There are 70 samples that pass purity filtering "
[1] "Tissue type:  tumor  "
[1] "Get final data..."
[1] "Saving table..."
[1] "LOG: Table dimensions: 20266 x 65 "
[1] "DONE!"
[1] "Saving RDS..."
